title: H_NS3

city: Utrecht

first: Marcel

last: de Zoete

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

data_processing:
Each sample gave a minimum of 6 GB of raw data with a Q30 ≥80%. FastQ files were used for alignment to the human genome using HISAT2 and counts were determined using featureCounts
Supplementary files format and content: combined_counts_symbol.csv, tab-delimited csv file including raw counts for each sample

extract_protocol:
RNA was isolated Cells were washed twice with cold PBS and subsequently lysed in TRIzol (Invitrogen) and stored at -20 C. RNA isolation was performed according to the TRIzol RNA isolation protocol entirely for qPCR samples or until the phase separation step for the RNA-sequencing samples. Subsequently, for these samples the aqueous phase (containing the RNA) was transferred to an RNeasy mini kit (Qiagen) column to continue RNA isolation. Subsequently, RNeasy RNA isolation protocol was followed from the addition of 70% ethanol onwards. DNA contamination was removed using TURBO DNA-free Kit (Invitrogen) according to protocol.
RNA sample quality control, mRNA library preparation (poly A enrichment) and sequencing (Illumina NovaSeq PE150) was performed by Novogene

value: WT

value: no stimulation


title: H_NS2

status: Public on May 13 2024

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: genotype

tag: treatment


title: 64_GES15_02149_Islet

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

country: USA

institute: The Jackson Laboratory

data_processing:
Each tissue directory has a raw counts matrix, a vst matrix and mrna annotations table.  counts_matrix.csv: raw counts quantified by EMASE and processed by/RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script.  vst_matrix.csv: counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation). Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.  mrna_annots.csv: gene annotation file ENSEMBL version 75.
Assembly: GRCm38
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv

molecule: total RNA

organism: Mus musculus

source_name: Islet

extract_protocol:
RNA was isolated from pancreatic islets using the RNeasy Micro kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies)
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction. Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

treatment_protocol: Mice were sensitized on a high-fat, high-sugar (HFHS) diet

tag: tissue

value: Islet

tag: diet

value: 45percent  fat


title: Pol II NET-seq, untreated, replicate 3

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

description: WTC

data_processing:
*library strategy: NET-seq
Base-calling was conducted with bcl convert software.
Deduplication based on the UMI sequence was performed via fqtrim (version 0.9.7) with the "-C" option.
First trimming step was achieved via cutadapt (version 3.4) and the "-g -no-indels" parameters. Reads containing the 5' sequence 5'-AGNNNNNNNNTG-3' were isolated, and this sequence was removed.
Second trimming step was performed with cutadapt (version 3.4) and the "-a -no-indels" parameters. The 3' sequence 5'-CTGTAGGCACCAT-3' was removed from reads.
Reads were aligned to the Saccharomyces cerevisiae genome via STAR (version 2.7.1a). The STAR alignIntronMax parameter was set to 1.
Output BAM files from alignment were indexed using SAMtools (version 1.6).
The bamCoverage tool from the deepTools package was used to generate bigWig files, with parameters set to "--Offset 1 --normalizeUsing CPM".
The computeMatrix tool (scale-regions subtool) from the deepTools package with the parameters set to "-b 3000 -a 3000 --regionBodyLength 5000 --skipZeros" was used.
The plotProfile tool from the deepTools package was used to visualize data.
Assembly: S. cerevisiae R64-1-1
Supplementary files format and content: Processed data for each sample are included in an individual bigWig (.bw) file.

organism: Saccharomyces cerevisiae

source_name: untreated

growth_protocol: Yeast were grown at 30ºC with nutation.

extract_protocol:
Cell harvest, lysis, and RNA extraction were performed exactly the same as described in previous publications from our lab. To summarize, yeast cells were rapidly harvested via filtration and lysed under cryogenic conditions. Pol II was isolated via immunoprecipitation and an acidic phenol/chloroform extraction was used to extract total RNA.
NET-seq library construction was performed exactly as described in previous publications from our lab. To summarize, a UMI-containing DNA linker was ligated onto the 3' end of RNAs after the total RNA extraction. Next, reverse transcription was performed and resulting DNAs were circularized. Finally, circular DNAs were amplified, libraries were purified via PCRClean DX beads, and reads were sequenced with the Illumina NovaSeq 6000 machine.

treatment_protocol: Immediately prior to the immunoprecipitation, frozen cell lysates were resuspended in lysis buffer (5 mL * grindate weight; previously described in Clarke et al, PNAS (2018)). For CaCl2 treated samples, a final concentration of 5 mM of CaCl2 was added, then samples were mixed thoroughly and incubated at 37ºC for 2 minutes. To quench the reaction, a final concentration of 5 mM of EDTA (pH 8.5) was added. For the MnCl2 treated samples, a final concentration of 10 mM MnCl2 was added and samples were mixed well. Samples were incubated on ice for 20 minutes, then the reaction was quenched with the addition of 5 mM EDTA (pH 8.5). Finally, samples were incubated on ice for 30 minutes.

tag: cell type

value: untreated


title: KO_siC_TPL_1

city: Cambridge

first: Ana

last: Tufegdzic Vidakovic

state: Cambridge

address: Cambridge Biomedical Campus, Francis Crick Ave

country: United Kingdom

institute: MRC-LMB

data_processing:
*library strategy: transient transcriptome sequencing (TT-seq)
TTchem-seq reads were trimmed and quality-filtered with Trim Galore, using a quality threshold of 30. Trimmed reads were aligned to the hg38 and Saccharomyces cerevisiae (sacCer3) genomes using STAR aligner90 with basic two-pass mapping.
PCR duplicates were marked and removed using Picard, and the correlation between replicates was checked using deepTools multiBamSummary. Replicates were merged, and resulting BAM files were split by strand. Bigwig files were created using deepTools bamCoverage, normalising to the number of spike-in reads.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: Flp-In T-REx HEK293

growth_protocol: DMEM (31966047), 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37°C with 5% CO2.

extract_protocol:
RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) accordingly to the manufacturers instructions. As a control for equal sample preparation, we spiked-in S. cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) 4-thiouracil (4TU)-labelled RNA. For purification of 4sU labelled RNA, 100 ug mammalian 4SU labelled RNA was spiked-in with 1ug of 4tU-labelled S. cerevisiae RNA. The 101 ug RNA was fragmented by addition of 20 uL of 1 M NaOH to fragment RNA and left on ice for 20 min. Fragmentation was stopped by addition of 80 uL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin‚P-30 Gel Columns (BioRad, 7326223). Biotinylation of 4sU-residues were carried out in a total volume of 250 ul, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA, 50uL DMF and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65C and added to 200 uL uMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a uColumn in the magnetic field of a uMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4sU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
Libraries for RNA sequencing were prepared using the KAPA RNA HyperPrep Kit (KR1350) with modifications. 75 ng of RNA per sample were mixed with FPE Buffer, but fragmentation procedure was omitted and RNA was instead denatured at 65C for 5 min. The rest of the procedure was performed as recommended by the manufacturer, with the exception of SPRI bead purifications: after adaptor ligation, 0.95x and 1x SPRI bead-to-sample volume ratios were used (instead of two rounds of SPRI purification with 0.63x volume ratios). This was done to retain smaller (150-300 bp) cDNA fragments in the library which would otherwise be lost in size selection. The libraries were quality controlled by electrophoresis on a Tapestation system (Agilent), quantified by Qubit (Thermofisher).

treatment_protocol: For each condition, 2 wells of a 6-well plate were seeded, each containing 600,000 cells, and transfected with siRNAs (Dharmacon, L-020270-02 and D-001810-10) the next day, using Lipofectamine RNAiMax (Invitrogen, 13778100), according to manufacturers instructions. 40 nM final siRNA concentration was used. 24 hours after transfection, cells of the same condition were re-seeded and combined into a single 10cm dish. The following day, cells were treated with 300nM triptolide for2 hours or vehicle, and nascent RNA was in vivo labelled with a 1 mM 4sU (Glentham Life Sciences, GN6085) pulse for exactly 15 min (e.g. for 2-hour triptolide time point samples, 4sU was added 1 h and 45 min after treatment).

value: Flp-In T-REx HEK293

value: ARMC5 KO

value: siControl, triptolide


title: Total_PolII_WT_unt_rep3

library_source: genomic

data_processing:
*library strategy: dxChIP-seq
dxChIP-seq reads were trimmed and quality-filtered with Trim Galore using a quality threshold of 30.
Trimmed reads were aligned to the hg38 genome using Bowtie2 with default parameters, then PCR duplicates were marked and removed with Picard.
The correlation between replicates was checked using deepTools multiBamSummary, then replicates were merged.
Merged BAM files were converted into RPKM-normalised bigwigs using deepTools bamCoverage.
Assembly: GRCh38
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1.66 mM disuccinimidyl glutarate (DSG) for 15 minutes, followed by washing and fixing with 1% formaldehyde for 8 minutes at room temperature. After quenching and cell lysis, cells were sonicated using a Covaris E220 sonicator for 4 minutes.
dxChIP-seq samples were prepared using NEBNext Ultra II DNA Library prep kit and validated using bioanalyzer DNA High Sensitivity kit.

treatment_protocol: Cells were treated with vehicle or triptolide at 300 nM for 2 h.

value: Parental WT

tag: chip antibody


title: H_NS1


title: 63_GES15_02148_Islet


title: Pol II NET-seq, untreated, replicate 2

description: WTB


title: 62_GES15_02147_Islet


title: Total_PolII_WT_unt_rep2


title: Pol II NET-seq, untreated, replicate 1

description: WTA


title: H_F3

value: flagellin


title: 61_GES15_02146_Islet


title: BHLKO_CT16_21C

city: Rehovot

first: Vaishnavi

last: Dandavate

address: 26B Arthur Ruppin street

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome /shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count in union mode.
Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2 with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg
Assembly: mm10
Supplementary files format and content: xlsx files containing the raw counts and normalized counts for each gene and sample

source_name: Liver

growth_protocol: 3-5 months old mice were housed under standard light-dark conditions (12h/12h) for 2 weeks before the experiment, till the day of the experiment.

extract_protocol:
Tissues were snap-frozen in liquid nitrogen immediately after dissection and stored at -80°C till used. For RNA extraction, the tissues were soaked in TRI-reagent (Sigma) and were homogenized by bead beater (Bead Ruptor e24, OMNI), and then proceeded by a standard TRI-reagent based RNA extraction protocol. RNA concentration was determined using NanoDrop™ 2000 Spectrophotometer (Thermo Fisher Scientific). RNA Integrity was validated using 2200 TapeStation (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lights were turned off at the transition of dark to light regiment on the day of the experiment following regular LD regimen, food served ad libitum

value: Liver

tag: strain

tag: ct

value: Alb-Cre+ Bmal1fl/fl  Hif1afl/fl

value: 21 percent oxygen


title: Total_PolII_WT_TPL_rep3

value: triptolide


title: Total_PolII_WT_unt_rep1


title: 59_GES15_02144_Islet


title: Total_PolII_WT_TPL_rep2


title: BHLKO_CT16_21B


title: H_F1


title: BHLKO_CT16_21A


title: H_F2


title: 57_GES15_02142_Islet


title: 58_GES15_02143_Islet


title: BLKO_CT16_6C

description:
4 hours oxygen exposure at respective CT
AlbCRE_HLKO_BLKO_Hypoxia_RNASeq_reads.xlsx

value: Alb-Cre+ Bmal1fl/fl

value: 6% oxygen


title: Total_PolII_WT_TPL_rep1


title: H_AH1

value: ADP-heptose


title: 56_GES15_02141_Islet


title: BLKO_CT16_6B


title: Total_PolII_ARMC5_KO_unt_rep3


title: 55_GES15_02140_Islet


title: BLKO_CT16_6A


title: Total_PolII_ARMC5_KO_unt_rep2


title: 54_GES15_02139_Islet


title: Total_PolII_ARMC5_KO_unt_rep1


title: U2OS MDM2 W329G cells #2, 5-FU, 24 hours, experiment 2

city: New York

first: Dr. Liang

last: Lei

state: NY

address: 1130 St. Nicholas Ave

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
Raw reads were mapped to hg19 Illumina iGenomes annotation
Assembly: hg19
Supplementary files format and content: fastq file includes raw data for each sample
Supplementary files format and content: tab-delimited text with counts output includes processed data for each sample

growth_protocol: U2OS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C,  5% CO2.

extract_protocol:
RNA was extracted with Qiagen RNeasy mini kit
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit.

treatment_protocol: Cells were treated with DMSO or 5-FU (50 µM) for 24 hours

value: human osteosarcoma cells

value: MDM2 W329G


title: Total_PolII_ARMC5_KO_TPL_rep3


title: BLKO_CT16_21C

value: 21% oxygen


title: U2OS MDM2 W329G cells #1, 5-FU, 24 hours, experiment 2


title: BLKO_CT16_21B


title: Total_PolII_ARMC5_KO_TPL_rep2


title: U2OS wild-typle cells #2, 5-FU, 24 hours, experiment 2

value: WT


title: 52_GES15_02137_Islet

value: Islet

value: 45percent  fat


title: Total_PolII_ARMC5_KO_TPL_rep1

value: Flp-In T-REx HEK293

value: ARMC5 KO


title: 53_GES15_02138_Islet


title: H_AH3


title: U2OS wild-typle cells #1, 5-FU, 24 hours, experiment 2


title: H_AH2


title: BLKO_CT16_21A


title: S5P_WT_unt_rep3

value: Parental WT

value: 3E8, Dirk Eick

value: untreated


title: 50_GES15_02135_Islet


title: U2OS MDM2 W329G cells #2, DMSO, 24 hours, experiment 2

value: DMSO, 24 hr


title: BLKO_CT4_6A

value: Liver


title: 49_GES15_02134_Islet


title: S5P_WT_unt_rep2


title: U2OS wild-typle cells #2, DMSO, 24 hours, experiment 2


title: U2OS MDM2 W329G cells #1, DMSO, 24 hours, experiment 2


title: 48_GES15_02133_Islet


title: S5P_WT_unt_rep1


title: BLKO_CT4_21C


title: U2OS wild-typle cells #1, DMSO, 24 hours, experiment 2


title: S5P_WT_TPL_rep3

value: triptolide


title: 47_GES15_02132_Islet


title: S5P_WT_TPL_rep2


title: BLKO_CT4_6C

value: Alb-Cre+ Bmal1fl/fl


title: 51_GES15_02136_Islet


title: 46_GES15_02131_Islet


title: BLKO_CT4_21B


title: U2OS MDM2 W329G cells #2, 5-FU, 24 hours, experiment 1


title: HLKO_CT16_6C

value: Alb-Cre+ Hif1afl/fl

value: 6% oxygen


title: S5P_WT_TPL_rep1


title: HLKO_CT16_6B


title: BLKO_CT4_6B


title: 44_GES15_02129_Islet


title: U2OS wild-typle cells #2, 5-FU, 24 hours, experiment 1

value: human osteosarcoma cells


title: S5P_ARMC5_KO_unt_rep2


title: 45_GES15_02130_Islet


title: U2OS wild-typle cells #1, 5-FU, 24 hours, experiment 1


title: S5P_ARMC5_KO_unt_rep3


title: U2OS MDM2 W329G cells #2, DMSO, 24 hours, experiment 1

value: MDM2 W329G


title: 42_GES15_02127_Islet


title: HLKO_CT16_6A


title: HLKO_CT16_21C

value: 21% oxygen


title: U2OS MDM2 W329G cells #1, DMSO, 24 hours, experiment 1


title: S5P_ARMC5_KO_TPL_rep3


title: S5P_ARMC5_KO_unt_rep1


title: 41_GES15_02126_Islet


title: HLKO_CT16_21B


title: S5P_ARMC5_KO_TPL_rep2


title: BLKO_CT4_21A


title: 40_GES15_02125_Islet


title: U2OS wild-typle cells #1, DMSO, 24 hours, experiment 1

value: WT


title: U2OS wild-typle cells #2, DMSO, 24 hours, experiment 1


title: HLKO_CT16_21A


title: 43_GES15_02128_Islet

value: Islet


title: HLKO_CT4_6C


title: U2OS MDM2 W329G cells #1, 5-FU, 24 hours, experiment 1


title: S5P_ARMC5_KO_TPL_rep1


title: 39_GES15_02124_Islet

value: 45percent  fat


title: HLKO_CT4_6B


title: HLKO_CT4_6A


title: 37_GES15_02122_Islet


title: Input_WT_unt_rep3

value: Flp-In T-REx HEK293


title: Input_WT_unt_rep1


title: WT_4

first: Nefeli

last: Skoufou-Papoutsaki

address: Robinson Way

institute: University of Cambridge

description:
idtUDP0015
WT_4

data_processing:
The reads were quantified against the human genome assembly GRCh38 using Salmon
The DEseq2 package (version 1.26.0)  was used for differential expression analysis
Assembly: GRCh38
Supplementary files format and content: allRawCounts.csv:raw counts for each sample after alignment
Supplementary files format and content: normalizedCounts.csv: counts for all samples after normalisation which was directly used to perform the differential gene expression analysis

source_name: colon

extract_protocol:
Arcturus PicoPure RNA extraction kit (Thermofisher, KIT0204)
6000 Nano Kit- Total Eukaryotic RNA

value: colon


title: PTEN_het_2

description:
idtUDP0065
PTEN_het_2


title: PTEN_KO_3

description:
idtUDP0016
PTEN_KO_3


title: Input_WT_unt_rep2

value: Parental WT


title: 36_GES15_02121_Islet


title: Input_WT_TPL_rep3


title: HLKO_CT4_21C


title: PTEN_KO_2

description:
idtUDP0013
PTEN_KO_2


title: PTEN_het_4

description:
idtUDP0014
PTEN_het_4


title: 35_GES15_02120_Islet


title: 34_GES15_02119_Islet


title: HLKO_CT4_21B


title: Input_WT_TPL_rep2


title: ARID1A_het_3

description:
idtUDP0012
ARID1A_het_3


title: 32_GES15_02117_Islet


title: HLKO_CT4_21A


title: Input_WT_TPL_rep1


title: 38_GES15_02123_Islet


title: WT_3

description:
idtUDP0010
WT_3


title: Alb_CT16_6C

value: Alb-Cre


title: Input_ARMC5_KO_unt_rep3

value: ARMC5 KO

value: untreated


title: 31_GES15_02116_Islet


title: Alb_CT16_6B

value: Liver


title: 30_GES15_02115_Islet


title: ARID1A_het_2

description:
idtUDP0009
ARID1A_het_2


title: Input_ARMC5_KO_unt_rep2


title: Alb_CT16_6A


title: 29_GES15_02114_Islet


title: Alb_CT16_21C


title: 28_GES15_02113_Islet


title: PTEN_het_1

description:
idtUDP0007
PTEN_het_1


title: Input_ARMC5_KO_TPL_rep3

value: triptolide


title: PTEN_KO_1

description:
idtUDP0006
PTEN_KO_1


title: Alb_CT16_21B


title: 27_GES15_02112_Islet


title: Input_ARMC5_KO_TPL_rep2


title: WT_2

description:
idtUDP0005
WT_2


title: Alb_CT16_21A


title: Input_ARMC5_KO_TPL_rep1


title: 26_GES15_02111_Islet


title: Alb_CT4_6C


title: ARID1A_het_4

description:
idtUDP0003
ARID1A_het_4


title: 24_GES15_02109_Islet


title: 50K-C004, S4

city: Milan

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

country: Italy

institute: CNR and Istituto Nazionale Genetica Molecolare

data_processing:
Trimming. High-throughput sequencing reads were trimmed using Trimmomatic (v0.39) (Bolger, Lohse, and Usadel 2014) using the following parameters: 2 for seed_mismatch, 30 for palindrome_thresh old, 10 for simple_threshold, 3 for leading, 3 for trailing and 4:15 for sliding window. The sequence minimum length threshold of 35 was applied to all data sets. We used the Trimmomatic “TruSeq3 - SE.fa” (for single end).
Alignment. After trimming, reads were aligned using BWA (v0.7.17 - r1188) (Li and Durbin 2009) setting – k parameter as 2 and using as reference genome the UCSC hg38 genome (only canonical chromosomes were used) and the output saved in BAM file format.
Filtering. The PCR duplicates were marked with Picard (v2.22; https://github.com/broadinstitute/picard) MarkDupuplicates option, then filtered using Samtools (v1.9) (Li et al. 2009). In addition, we filtered all the reads with mapping quality lower than 1. Each sequencing lane was analyzed separately and then merged at the end of the process.
Genomic tracks. To compute reads distribution profile (genomic tracks) we used Deeptools (v3.4.3) (Ramirez et al. 2016) bam Coverage function. For these analyses the genome was binned at 50bp, the reads extended up to 250 bp and RPKM normalization method was used. We considered a genome size of 2701495761 bp (value suggested in the Deeptools manual https://deeptools.readthedocs .io/en/latest/content/feature/effectiveGenomeSize.html) and we excluded regions known to be problematics in term of sequencing reads coverage using the black list from the ENCODE portal (https://www.encodeproject.org/files/ENCFF356LFX/)
Assembly: hg38
Supplementary files format and content: Bigwiggle files (.bw) are created using Deeptools for genomic track data
Library strategy: SAMMY-seq

source_name: patient derived foreskin fibroblasts

growth_protocol: Cells were cultured at 37 °C, 5% CO2 in DMEM high glucose supplemented with GlutaMAX (Gibco,10566-016), with further addition of 15% (v/v) FBS (Gibco, 10270106), 100 U/mL penicillin G and 100 μg/mL Streptomycin Sulfate.

extract_protocol:
For 4f-SAMMY-seq,10,000 (10k) or 50,000 (50k) fibroblasts were detached from the culture plate by 3min incubation in Trypsin-EDTA solution at 37°C, 5% CO2. After two washes in cold PBS, the cells were resuspended in 600μL of CSK-Triton buffer (10mM PIPES pH 6.8, 100mM NaCl, 1mM EGTA, 300mM Sucrose, 3mM MgCl2, 1mM PMSF, 1mM DTT, 0.5% Triton X-100, with protease inhibitors). After 10min incubation on a wheel at 4°C, soluble proteins and the cytoskeletal structure were separated from the nuclei by centrifugation at 900g for 3min at 4°C; the supernatant was labelled as S1 fraction. The pellet was then washed with an additional volume of CSK-Triton buffer, resuspended in 100μL of CSK buffer (10mM PIPES pH 6.8, 100mM NaCl, 1mM EGTA, 300mM Sucrose, 3mM MgCl2, 1mM PMSF, with protease inhibitors) and incubated for 60min at 37°C with 2U of RNase–free DNase I (Invitrogen, AM2222).To stop DNA digestion, ammonium sulphate was added in the CSK buffer to a final concentration of 250mM. After 5min incubation on ice, the sample was pelleted at 900g for 3min at 4°C; the supernatant, containing digested chromatin fragments, was labelled as S2 fraction. Afterwards, the pellet was washed with 200μL of CSK buffer and pelleted at 3000g for 3min at 4°C, then resuspended in 100μL of CSK-NaCl buffer (CSK buffer with NaCl final concentration increased to 2M) and incubated for 10min on a wheel at 4°C. At the end of the incubation, the sample was centrifuged at 2300g for 3min at 4°C and the supernatant was labelled as S3 fraction. Finally, after two 10min washes in 200μL of CSK-NaCl buffer on a wheel at 4°C followed by centrifugation at 3000g for 3min at 4°C, the pellet was solubilized in 100μL of 8M urea; the final suspension was labelled as S4 fraction. Fractions S2, S3 and S4 were diluted in TE (10mM TrisHCl pH 7.5, 1mM EDTA pH 8.0) to a final volume of 200μl and then incubated 90min at 37°C with 6μL of RNAse cocktail (Ambion, AM2286), followed by 150min at 55° with Proteinase K (Invitrogen, AM 2548) to a final concentration of 0.2 μg/μL. Next, DNA was isolated through phenol:chloroform:isoamyl alcohol (Sigma, 77617) extraction, precipitated in 70% ethanol, 0.3 M sodium acetate and 20 μg glycogen overnight at -20°C or 1 hour in dry ice and resuspended in nuclease-free water. S2 was additionally purified using PCR DNA Purification Kit (Qiagen, 28106) and then DNA fragments in this fraction were separated using AMPure XP paramagnetic beads (Beckman Coulter, A63880) to obtain S2S (<300bp) and S2L (> 300bp) fractions. In detail, beads were added to the S2 fraction in a 0.95x (v/v) ratio, so to bind fragments larger than 300bp while leaving smaller fragments in solution. Magnetic separation of beads from supernatant allowed the physical separation of larger fragments (on the beads) from shorter ones (in the supernatant). Larger fragments bound on the beads were then washed in 85% ethanol, resuspended in water and magnetically separated from the beads (S2L fraction). Shorter fragments in the supernatant of the first step were bound to beads by adding a further 0.85x (v/v) beads ratio to the suspension; after washing in 85% ethanol and resuspending in water, they were also detached from the beads (S2S fraction). After DNA isolation, S2L, S3 and S4 fractions were transferred to screw cap microTUBEs (Covaris, 004078) and sonicated in a Covaris M220 focused-ultrasonicator to obtain a smear of DNA fragments peaking at 200bp (settings: water bath 20°C, peak power 30.0, duty factor 20.0, cycles/burst 50; duration: 125sec for S2 and S2L, 175sec for S3 and S4). DNA in the fractions was then quantified using Qubit dsDNA HS Assay Kit (Invitrogen, Q32854) and a Qubit 4.0 fluorometer; quality control was performed by run on an Agilent 2100 Bioanalyzer System using the High Sensitivity DNA Kit (Agilent, 5067-4626).
Libraries were created from each fraction using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) and the Unique Dual Index NEBNext Multiplex Oligos for Illumina (NEB, E6440S).

treatment_protocol: No treatment has been performed on these cells.

value: patient derived foreskin fibroblasts

tag: number of_cells

tag: fraction


title: Alb_CT4_6B


title: ARID1A_het_1

description:
idtUDP0008
ARID1A_het_1


title: 50K-C004, S3


title: PTEN_het_3

description:
idtUDP0004
PTEN_het_3


title: Alb_CT4_6A


title: 50K-C004, S2S


title: 23_GES15_02108_Islet


title: 25_GES15_02110_Islet


title: PTEN_KO_4

description:
idtUDP0002
PTEN_KO_4


title: Input_ARMC5_KO_unt_rep1


title: Alb_CT4_21C


title: Alb_CT4_21B


title: WT_1

description:
idtUDP0001
WT_1


title: 50K-C004, S2L


title: 21_GES15_02106_Islet


title: 10K-C004, S4


title: Alb_CT4_21A


title: ASIBEL-2

city: salt lake city

first: Mahesh

middle: Babu

last: Chandrasekharan

state: Utah

address: 2000 circle of hope room 3715

department: Radiation Oncology

institute: University of Utah SOM

data_processing:
Fastq files were trimmed with Cutadapt (version 1.16) and aligned to the human genome (Ensembl GRCh38, release 96) using the STAR aligner (version 2.7.0) with basic two-pass mode.
Paired alignment counts were collected with Subread featureCounts (version 1.6.3) with options for second-strand synthesis and only counting features with the largest overlap.
Assembly: GRCh38 Ensembl release 96
Supplementary files format and content: Text file containing gene fragment counts

source_name: Brain

growth_protocol: MTU87 and LTAU87 cells were cultured in DMEM media supplemented with 10% Fetal bovine serum and 1% penicillin-streptomycin media.

extract_protocol:
Total RNA was isolated using ROCHE HIPURE RNA isolation kit.
RNA was eluted in water and libraries were prepared using Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold.

treatment_protocol: MTU87 and LTAU87 cells were treated with 1uM belinostat for 24hr.

value: Brain

value: Brain cancer

value: Long-term AsiDNA treatment +Belinostat


title: 20_GES15_02105_Islet


title: ASIBEL-1


title: BEL-2

value: Belinostat


title: MicroglialCells_CB2r-/-, scRNAseq

city: Milwaukee

first: Anthony

middle: Elston

last: Zamora

state: Wisconsin

address: 8701 Watertown Plank Road

department: Medicine

institute: Medical College of Wisconsin

description:
10x Genomics
instrument model: G4 sequencer from Singular Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v.7.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Microglial cells

extract_protocol:
Cells were isolated from the brains of mice, sorted for the live cells, resuspended in PBS with 2% BSA at a concentration of 700-800 cells per microliter and used as input for a target recovery of 5000 cells.
Library was performed according to Chromium Next GEM Single Cell 5' Reagent kits v2 and Chromium GEM Single Cell 3' Reagent kit v3. Specifically the sequencing of immune populations in the brain from BM control versus GVHD animals was done using Chromium Next GEM Single Cell 5' reagent kit v2, while sequencing of microglia from WT and CB2R-/- mice was done using the chromium single cell 3' reagent kits v3.

value: Microglial cells

tag: condition


title: 10K-C004, S3


title: 10K-C004, S2S


title: 19_GES15_02104_Islet


title: MicroglialCells_WT, scRNAseq

value: WT


title: BEL-1


title: ImmuneCells_GVHD, scRNAseq

source_name: Immune cells

value: Immune cells

value: GVHD


title: C004-r2_10Kh_S4

data_processing:
Trimming. High - throughput s equencing reads were trimmed using Trimmomatic (v0.39) (Bolger, Lohse, and Usadel 2014)  using the following parameters: 2 for seed_mismatch, 30 for palindrome_thresh old, 10 for simple_threshold, 3 for leading, 3 for trailing and 4:15 for sliding window. The sequence minimum length threshold of 35 was applied to all data sets . We used the Trimmomatic “TruSeq3 - SE.fa” (for single end) and “TruSeq3 - PE - 2.fa” (for paired end) as clip files .
Alignment. After trimm ing, reads were aligned using BWA (v0.7.17 - r1188) (Li and Durbin 2009) setting – k parameter as 2 and using as reference genome the UCSC hg38 genome (only canonical chromosomes were used ) and the output saved in BAM file format .
Filtering. The PCR duplicates were marked with Picard (v2.22; https://github.com/broadinstitute/picard) MarkDupuplicates option , then filtered using Samtools (v1.9) (Li et al. 2009) . I n addition, we filtered all the reads with mapping quality lower than 1. Each sequencing lane was analyzed separately and then merged at the end of the process. For C002 - rep1 and C004 - rep2 two sequencing runs from the same library were produced and merged after alignment and filtering.
Genomic tracks. To compute reads distribution profile (genomic tracks) we used Deeptools (v3.4.3) (Ramirez et al. 2016) bam Coverage function. For these analyses the genome was binned at 50bp, the reads extended up to 250 bp and RPKM normalization method was used. We considered a genome size of 2701495761 bp (value suggested in the Deeptools manual https://deeptools.readthedocs .io/en/latest/content/feature/effectiveGenomeSize.html) and we excluded regions known to be problematics in term of sequencing reads coverage using the black list f rom the ENCODE portal ( https://www.encodeproject.org/files/ENCFF356LFX/ )
Comparisons. for relative comparisons (relative enrichment , i.e. log2 normalized ratio) between SAMMY - seq fraction s we us ed the SPP R package (v1.16.0) (Kharchenk o, Tolstorukov, and Park 2008) and R statistical environment (v3.5.2). The reads were imported from the BAM files using the “read.bam.tags” function, then filtered using “remove.local.tag.anomalies” and finally the comparison s performed using the function “get.smoothed.enrichment.mle” setting “tag.shift = 0” and “background.density.scaling = TRUE”. The resulting enrichment signal correspond s to a log2 normalized ratio between the pair of sequencing samples.
Assembly: hg38
Supplementary files format and content: Bigwiggle files (.bw) are created using Deeptools for genomic track data and with wigToBigWig (v4) starting from wiggle files generated by SPP for what concern comparisons.

source_name: skin fibroblast

growth_protocol: Cells were cultured at 37 °C, 5% CO2in DMEM high glucose supplemented with GlutaMAX(Gibco,10566-016), with further addition of 15% (v/v) FBS (Gibco, 10270106), 100 U/mL penicillin G and 100 μg/mLStreptomycin Sulfate.

extract_protocol:
For 4f-SAMMY-seq, 3 million fibroblasts were detached from the culture plate by 3 min incubation in trypsin-EDTA at 37°C, 5% CO2. After two washes in cold PBS, they were resuspended in 600 μL ofCSK-Triton buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 1 mM EGTA, 300 mM Sucrose, 3 mM MgCl2, 1mM PMSF, 1 mM DTT, 0.5% Triton X-100, with protease inhibitors). After 10 min incubation on a wheel at 4°C, soluble proteins and the cytoskeletal structure were separated from the nuclei by centrifugation at 900g for 3 min at 4°C; the supernatant was labeled as S1 fraction. The pellet was then washed with an additional volume of CSK-Triton buffer, resuspended in 100 μL of CSK buffer (10 mM PIPES pH 6.8, 100 mMNaCl, 1 mM EGTA, 300 mM Sucrose, 3 mM MgCl2, 1mM PMSF, with protease inhibitors) and incubated for 60 min at 37°C with 25 U of RNase–free DNase I (Invitrogen, AM2222). To stop DNA digestion, ammonium sulphate was added in the CSK buffer to a final concentration of 250 mM. After 5 min incubation on ice, the sample was pelleted at 900g for 3 min at 4°C; the supernatant, containing digested chromatin fragments, waslabeled as S2 fraction. Afterwards, the pellet was washed with 200 μL of CSK buffer, resuspended in 100 μL of CSK-NaCl buffer (CSK buffer with NaCl final concentration increased to 2 M) and then incubated 10 min on a wheel at 4°C. At the end of the incubation, the sample was centrifuged at 2300g for 3 min at 4°C and the supernatant was labeled as S3 fraction. Finally, after two washes in 200 μL of CSK-NaCl buffer, the pellet was solubilized in 100 μL of 8M urea; the final suspension was labeled as S4 fraction. For 10kh-SAMMY-seq, 10 thousand fibroblasts were treated following 4f-SAMMY-seq protocol, halving the volume in each step and using 12.5U of DNAse I (Invitrogen, AM2222); in this way we achieved a 150 fold increase in the ratio of enzyme units per starting number of cells, while maintaining the DNase concentration unaltered. Fractions S2, S3 and S4 were diluted in TE (10 mM TrisHCl pH 7.5, 1mM EDTA pH 8.0) to a final volume of 200 μl and then incubated 90 min at 37°C with 6 μL of RNAse cocktail (Ambion, AM2286), followed by 150 min at 55° with Proteinase K (Invitrogen, AM 2548) to a final concentration of 0.2 μg/μL. Next, DNA was isolated through phenol:chloroform:isoamyl alcohol (Sigma, 77617), precipitated and resuspended in nuclease-free water. On the next day, S2 from 4f-SAMMY-seq was additionally purified using PCR DNA Purification Kit (Qiagen, 28106) and DNA fragments in this fraction were separated using AMPure XP paramagnetic beads (Beckman Coulter, A63880) to obtain S2S (< 300 bp) and S2L (> 300 bp) fractions. Beads were added to the S2 fraction in a 0.95x (v/v) ratio, so to bind fragments larger than 300bp. Magnetic separation of beads from supernatant allowed the physical separation of larger fragments (on the beads) from shorter ones (in the supernatant). Larger fragments bound on beads were then washed in 85% ethanol, resuspended in water and magnetically separated from the beads (S2L fraction). Shorter fragments in the supernatant of the first step were bound to beads by adding a further 0.85x (v/v) beads ratio to the suspension; after washing in 85% ethanol and resuspension in water, they were also detached from beads (S2S fraction). Afterwards, S2 (from 10kh-SAMMY-seq), S2L (from 4f-SAMMY-seq), S3 and S4 (from both 10kh- and 4f-SAMMY-seq) fractions were transferred to screw cap microTUBEs (Covaris, 004078) and sonicated in a Covaris M220 focused-ultrasonicator to obtain a smear of DNA fragments peaking at 200 bp (settings: water bath 20°C, peak power 30.0, duty factor 20.0, cycles/burst 50; duration: 125 sec for S2 and S2L, 175 sec for S3 and S4). Fractions were quantified using Qubit dsDNA HS Assay Kit (Invitrogen, Q32854 ) and a Qubit 4.0 fluorometer; quality control was performed by running them on an Agilent 2100 Bioanalyzer System using the High Sensitivity DNA Kit (Agilent, 5067 – 4626).
Libraries were then created from each fraction using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) and the Unique Dual Index NEBNext Multiplex Oligos for Illumina (NEB, E6440S).

value: patient derived skin fibroblast

tag: passage

tag: protocol

tag: sample


title: ASI-2

value: Long-term AsiDNA treatment


title: 16_GES15_02101_Islet

value: Islet

value: 45percent  fat


title: 22_GES15_02107_Islet


title: ImmuneCells_BM, scRNAseq

value: BM


title: 18_GES15_02103_Islet


title: ASI-1

value: Long-term AsiDNA treatement


title: 10K-C004, S2L


title: DMSO-2

value: DMSO


title: Liver_HFD_KO_rep6

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

description:
HFD_KO-6
HFD_counts.txt

data_processing:
the libraries were sequenced using the Illumina HiSeq X Ten system. We calculated Transcripts Per Million (TPM) values for each gene using the kallisto software, with the mm10 gene annotation file from GENCODE, employing the default parameters. Subsequently, we employed the DESeq2 package for differential gene expression analysis
Assembly: mm10
Supplementary files format and content: raw counts

extract_protocol: For RNA-seq experiments, ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (New England Biolabs, E7420) and TruSeq Stranded Total RNA Sample Prep kit (New England Biolabs, E6100)

value: Liver

tag: shfalcor

value: Falcor KO


title: C004-r2_10Kh_S2


title: C004-r2_10Kh_S3


title: 17_GES15_02102_Islet


title: 13_GES15_02098_Islet


title: C004-r2_4f_S4 (single-end)


title: Liver_HFD_KO_rep4

description:
HFD_KO-4
HFD_counts.txt


title: Liver_HFD_KO_rep5

description:
HFD_KO-5
HFD_counts.txt


title: 12_GES15_02097_Islet


title: Liver_HFD_KO_rep3

description:
HFD_KO-3
HFD_counts.txt


title: 11_GES15_02096_Islet


title: C004-r2_4f_S2S (single-end)


title: H1.2 CHIP from LTA U87 cells treated with 1uM Belinostat. Replicate 2.

data_processing:
Fastq files were aligned to a combined human (UCSC hg38) and Drosophila (UCSC dm6) genome index with Novocraft Novalign (version 4.0.1) with tuned parameters for Illumina Noaseq and simultaneous adapter trimming. Alignments from separate sequencing flow cells were merged.
Optical duplicates (pixel distance of 10000) were removed and excessive duplicates randomly subsampled to a uniform 1% rate relative to unique alignments using bam_partial_dedup (MultiRepMacsChIPSeq package, version 14).
Fragment coverage was generated using bam2wig (BioToolBox, version 1.68). Replicates were depth-normalized and averaged into a single file. Only properly-paired alignments with an insert size of 50-600 bp were used. Alignments overlapping Encode black list regions were skipped.
Assembly: Hg38
Supplementary files format and content: bigWig fragment coverage files normalized to 1 million fragments (RPM)

growth_protocol: MTU87 and LTAU87 cells were cultured in DMEM supplemented with 10% Fetal bovine serum and 1% penicillin-streptomycin media.

extract_protocol:
Drosophila S2 cells were mixed with human cells after collection. Cells were fixed with 1% formaldehyde for 10 min and sonicated using the Bioruptor Pico. Histone H1.2 antibody (Abcam ab17677) was used in immunoprecipitation and ChIP DNA
Library preparation was done with NEBNext Ultra II DNA Library Prep kit (cat#E7634L).

value: Brain

value: Glioblastoma

value: AsiDNA and Belinostat


title: H1.2 CHIP from LTA U87 cells treated with DMSO. Replicate 2.

value: AsiDNA and DMSO


title: Liver_HFD_KO_rep2

description:
HFD_KO-2
HFD_counts.txt


title: C004-r2_4f_S2L (single-end)


title: 10_GES15_02095_Islet


title: H1.2 CHIP from MT U87 cells treated with DMSO. Replicate 2.


title: Liver_HFD_KO_rep1

description:
HFD_KO-1
HFD_counts.txt


title: DMSO-1

value: Brain cancer


title: 15_GES15_02100_Islet


title: 9_GES15_02094_Islet


title: H1.2 CHIP from LTA U87 cells treated with 1uM Belinostat. Replicate 1.

value: WT


title: Liver_HFD_Ctrl_rep4

description:
HFD_Ctrl-5
HFD_counts.txt

value: Ctrl


title: Liver_HFD_Ctrl_rep5

description:
HFD_Ctrl-6
HFD_counts.txt


title: patient_MPRA_rep4

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

data_processing:
Sequencing data from the plasmid DNA and cDNA libraries described above were processed with cutadapt to remove adapters (Martin, 2011).
Barcodes were extracted using UMI-tools (Smith et al., 2017)
Reads were mapped using bwa mem (Li and Durbin, 2009) and assigned to caMPRA probes using featureCounts (Liao et al., 2014).
Barcodes for plasmid and cDNA samples were normalized to a barcode per million format to remove bias due to sequencing coverage. Each cDNA barcode was normalized to the barcode count in the plasmid pool, and log2 transformed. Only barcodes that were found in the plasmid pool and all 6 cDNA replicate pools were used in the analysis. Enhancer activity was assessed with the wilcoxon test at 5% FDR.
Assembly: hg19
Supplementary files format and content: xlsx file of patient MPRA results for HARs, VEs, and CNEs
Library strategy: MPRA

source_name: Neuro2A/N2A cells (ATCC, CCL-131)

growth_protocol: Neuro2A/N2A cells (ATCC, CCL-131) were grown in 10% fetal bovine serum, Dulbecco’s Modified Eagle Medium, and 1% Penicillin-Streptomycin in a 5% CO2 incubator at 37C.

extract_protocol:
Cell pellets were washed with 1x PBS, and mRNA was extracted using the Dynabead mRNA Direct kit (Thermo Fisher, cat #61012), according to the manufacturer’s instructions.
mRNA was reverse transcribed using Superscript VILO Master Mix with EZ DNase (Thermo Fisher, cat #11766050). caMPRA barcodes were extracted using PCR amplification with primers containing illumina adapters for both the cDNA and plasmid pools and sent out for 150bp sequencing using Hiseq instruments at Psomagen (Rockville, MD).

treatment_protocol: An oligo pool containing 238bp sequences centered on each of the 1,693 rare, recessive variants identified in HARs, VEs, or CNEs in the HMCA cohort and in HARs or VEs in the NIMH cohort with or without the variant of interest was synthesized by Twist Biosciences. Each sequence was represented 10 times in the oligo pool with different 12-mer barcodes. The oligo pool was amplified with PCR primers to add SfiI restriction sites, and then cloned and tested as previously described (Girskis et al., 2021). Briefly, the captures were cloned into modified pMPRA1 vector (Addgene, 49349). The only modification to the pMPRA1 vector was the addition of an AsiSI restriction site used for inserting our captured DNA fragments. The luciferase gene and minimal promoter (pMPRA_donor2, Addgene, 49353) was then cloned into the pMPRA1_Capture construct pool. N2A cells were grown as adherent cultures in 15 cm plates. Then, 15ug of MPRA constructs were transfected into cells with Lipofectamine LTX reagent (Thermo Fisher, A12621). The cells were harvested 72 hr post-transfection. Six replicates were performed.

value: Neuro2A/N2A cells (ATCC, CCL-131)


title: patient_MPRA_plasmid_DNA


title: 8_GES15_02093_Islet


title: H1.2 CHIP from MT U87 cells treated with 1uM Belinostat. Replicate 1

value: Belinostat


title: C004-r2_4f_S3  (single-end)

value: patient derived skin fibroblast


title: 6_GES15_02091_Islet

value: Islet


title: 7_GES15_02092_Islet

value: 45percent  fat


title: Liver_HFD_Ctrl_rep2

description:
HFD_Ctrl-2
HFD_counts.txt


title: patient_MPRA_rep3


title: H1.2 CHIP from LTA U87 cells treated with DMSO. Replicate 1.


title: Input from LTA U87 cells treated with 1uM Belinostat. Replicate 2.


title: 5_GES15_02090_Islet


title: H1.2 CHIP from MT U87 cells treated with 1uM Belinostat. Replicate 2.


title: Liver_HFD_Ctrl_rep1

description:
HFD_Ctrl-1
HFD_counts.txt


title: Liver_HFD_Ctrl_rep3

description:
HFD_Ctrl-4
HFD_counts.txt


title: patient_MPRA_rep2


title: 4_GES15_02089_Islet


title: Input from LTA U87 cells treated with DMSO. Replicate 2.


title: Liver_NCD_KO_rep4

description:
NCD_KO-5
NCD_counts.txt


title: patient_MPRA_rep5


title: patient_MPRA_rep6


title: Input from MT U87 cells treated with 1uM Belinostat. Replicate 2.


title: 3_GES15_02088_Islet


title: Liver_NCD_KO_rep3

description:
NCD_KO-4
NCD_counts.txt


title: patient_MPRA_rep1


title: Liver_NCD_KO_rep2

description:
NCD_KO-2
NCD_counts.txt


title: 2_GES15_02087_Islet


title: H1.2 CHIP from MT U87 cells treated with DMSO. Replicate 1.


title: Liver_NCD_KO_rep1

description:
NCD_KO-1
NCD_counts.txt


title: 3KO

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Brain endothelial cell

extract_protocol:
Total RNA was harvested by Trizol reagent.2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

tag: developmental stage


title: 1KO


title: 2Wildtype


title: 1_GES15_02086_Islet


title: Liver_NCD_Ctrl_rep4

description:
NCD_Ctrl-5
NCD_counts.txt


title: WSB_9_Adipose_GT19_34265

source_name: adipose

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step.
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction. Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

value: adipose

value: 45 percent fat


title: WSB_8_Adipose_GT19_34270


title: Input from LTA U87 cells treated with 1uM Belinostat. Replicate 1.

tag: cell line


title: Input from MT U87 cells treated with DMSO. Replicate 2.

tag: genotype

value: DMSO


title: Liver_NCD_Ctrl_rep3

description:
NCD_Ctrl-4
NCD_counts.txt

value: Liver


title: Input from MT U87 cells treated with DMSO. Replicate 1

tag: treatment


title: PDAC validation experiment 2, D7, row 5,cDNA

first: Alex

middle: K.

last: Shalek

state: MA

address: 77 Massachusetts Ave

institute: MIT

data_processing:
The demultiplexing, barcoded, processing, gene counting and aggregation were made using the STARsolo workflow (https://dockstore.org/workflows/github.com/lilab-bcb/cumulus/STARsolo:2.0.0?tab=info) and CITEseq-count (https://portal.firecloud.org/?return=terra#methods/bemead/CITEseq-count/7) on Terra
Assembly: hg38
Supplementary files format and content: tab separated value files and matrix files

source_name: pancreas

extract_protocol:
Patient-derived pancreatic cancer (PDAC) organoids were derived as previously described from patients with metastatic pancreatic cancer (Raghavan et al., Cell, 2021) and cultured in Growth factor Reduced Matrigel, fed with human complete organoid medium (Advanced DMEM/F12, 10 mM HEPES, 1x GlutaMAX, 500 nM A83-01, 50 ng/mL mEGF, 100 ng/mL mNoggin, 100 ng/mL hFGF10, 10 nM hGastrin I, 1.25 mM N-acetylcysteine, 10 mM Nicotinamide, 1x B27 supplement, RSPONDIN-1 conditioned media 10% final, WNT3A conditioned media 50% final, 100 U/mL penicillin/streptomycin, and 1x Primocin). Cells were seeded in seeded in 96-well plates and allowed to rest for 24 hours before ligand treatment where each well received 4 or 5 ligands in the compressed screen or only 1 ligand for the conventional validation screen. Assay plates were cultured for 7 days at 37°C/5% CO2 and processed for scRNA-seq with cell hashing.
PDAC organoids for compressed screens and validation experiments were transferred to the upper chamber of a 96 well filter plate on a vacuum manifold and media was aspirated under vacuum, to only retain organoids larger than 30-40 µms. Additional media was added and aspirated under vacuum to remove residual Matrigel and cell debris. Organoids were dissociated into single cells by resuspending with TrypLE Express for 20 minutes at 37°C with intermittent mixing. RPMI 1640 with 50 µg/mL DNase was added to quench digestion, and the single cell suspension was collected by centrifugation into a 96-well u-bottom ultra-low attachment plate and Quenching solution was aspirated. Cell staining solution (45uL cell staining buffer + 5uL human multiplexing antibody from BD Biosciences) was added to each well and incubated at room temperature for 20 minutes. Human multiplexing antibodies were distributed column-wise with each column having a unique tag, and samples were collapsed row-wise (containing non-overlapping tags). Usinng Honeycomb Bio HIVEs, 15,000 cells were loaded into each hive and the library was constructed following the Honeycomb Bio HIVE protocol as described in their October 2021 protocol (v21.10), with modifications to accommodate cell hashing.

tag: tissue

value: pancreas

value: PDAC organoid


title: 1Wildtype


title: WSB_7_Adipose_GT19_34196

tag: diet


title: Liver_NCD_Ctrl_rep2

description:
NCD_Ctrl-3
NCD_counts.txt


title: Liver_NCD_Ctrl_rep1

description:
NCD_Ctrl-2
NCD_counts.txt


title: PDAC validation experiment 2, D7, row 3,cDNA


title: WSB_5_Adipose_GT19_34149


title: Aml12_shCtrl _rep3

description:
Ctrl-3
sh_counts.txt

tag: cell type

value: shCtrl


title: Input from LTA U87 cells treated with DMSO. Replicate 1.

value: Brain

value: Glioblastoma


title: Patient7, post CART-cell Treatment, BCRseq

city: Berlin

first: Artur

last: Wilhelm

address: Virchowweg 11

department: Rheumatology and clinical immunology

country: Germany

institute: Charite Berlin

description: 10x Genomics

library_source: other

data_processing:
Demultiplexing, barcode processin, gene counting and clonotype calling was performed using the cellranger multi pipeline v.7.0.0.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab seperated matrix, gene and barcode files
Library strategy: TCR-seq

molecule: other

source_name: Blood

extract_protocol:
B cell enrichment was conducted using the EasySep™ Human B Cell Enrichment Kit (StemCell) in accordance with the manufacturer's instructions.
libraries were constructed using the Chromium Next GEM Single cell 5´Reagent Kits v2 (10 X Genomics)

value: Blood

value: B cells

value: post anti CD19 CART-cell therapy


title: Patient7, pre CART-cell Treatment, BCRseq

description: 10x Genomics

value: pre anti CD19 CART-cell therapy


title: Aml12_shCtrl _rep2

description:
Ctrl-2
sh_counts.txt


title: Patient6, pre CART-cell Treatment, BCRseq

description: 10x Genomics


title: Aml12_shCtrl _rep1

description:
Ctrl-1
sh_counts.txt


title: PDAC validation experiment 2, D7, row 1,cDNA


title: Patient6, post CART-cell Treatment, BCRseq

description: 10x Genomics


title: WSB_4_Adipose_GT19_34289

data_processing:
Each tissue directory has a raw counts matrix, a vst matrix and mrna annotations table.  counts_matrix.csv: raw counts quantified by EMASE and processed by/RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script.  vst_matrix.csv: counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation). Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.  mrna_annots.csv: gene annotation file ENSEMBL version 75.
Assembly: GRCm38
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv


title: Input from MT U87 cells treated with 1uM Belinostat. Replicate 1.

value: WT

value: Belinostat


title: PDAC validation experiment 2, D7, row 2,cDNA


title: Patient5, post CART-cell Treatment, BCRseq

description: 10x Genomics


title: WSB_3_Adipose_GT19_34251


title: WSB_1_Adipose_GT19_33944


title: PWK_9_Adipose_GT19_33953


title: PDAC validation experiment 2, D7, row 4,cDNA


title: Aml12_shZC3H11A _rep2

description:
Zc-2
sh_counts.txt


title: PDAC validation experiment 2, D7, row 3,hash

molecule: protein


title: WSB_6_Adipose_GT19_33800


title: Patient3, post CART-cell Treatment, BCRseq

description: 10x Genomics


title: PDAC validation experiment 2, D7, row 2,hash


title: PWK_6_Adipose_GT19_33875


title: PWK_5_Adipose_GT19_34092


title: Aml12_shFalcor _rep3

description:
L30-3
sh_counts.txt

value: shFalcor


title: Patient3, pre CART-cell Treatment, BCRseq

description: 10x Genomics


title: PDAC validation experiment 2, D7, row 5,hash


title: Aml12_shZC3H11A _rep3

description:
Zc-3
sh_counts.txt


title: PDAC validation experiment 2, D7, row 1,hash


title: Aml12_shFalcor _rep2

description:
L30-2
sh_counts.txt


title: Patient1, post CART-cell Treatment, BCRseq

description: 10x Genomics


title: PWK_4_Adipose_GT19_33795


title: PDAC validation experiment 1, D7, row 5,cDNA


title: Patient1, pre CART-cell Treatment, BCRseq

description: 10x Genomics


title: PDAC validation experiment 2, D7, row 4,hash


title: Patient5, pre CART-cell Treatment, BCRseq

description: 10x Genomics


title: PWK_7_Adipose_GT19_34235


title: PWK_3_Adipose_GT19_33854


title: PDAC validation experiment 1, D7, row 6,cDNA


title: Aml12_shZC3H11A _rep1

description:
Zc-1
sh_counts.txt


title: PDAC validation experiment 1, D7, row 4, cDNA


title: Aml12_shLinc_DoxPlus_rep2

description:
Aml12_inducible_17
Inducible_counts.txt

value: Add Dox


title: PWK_1_Adipose_GT19_33848

value: adipose


title: Aml12_shLinc_DoxPlus_rep3

description:
Aml12_inducible_18
Inducible_counts.txt


title: Patient7, pre CART-cell Treatment, scRNAseq

description: 10x Genomics

data_processing:
Demultiplexing, barcode processin, gene counting and clonotype calling was performed using the cellranger multi pipeline v.7.0.0.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab seperated matrix, gene and barcode files


title: Aml12_shLinc_DoxPlus_rep1

description:
Aml12_inducible_16
Inducible_counts.txt


title: PDAC validation experiment 1, D7, row3, cDNA


title: PWK_2_Adipose_GT19_33918

value: 45 percent fat


title: Patient6, post CART-cell Treatment, scRNAseq

description: 10x Genomics


title: PDAC validation experiment 1, D7, row 2,cDNA


title: NZO_7_Adipose_GT19_33834


title: Aml12_shCtrl_DoxPlus_rep2

description:
Aml12_inducible_14
Inducible_counts.txt


title: PDAC validation experiment 1, D7, row 1, cDNA


title: Aml12_shCtrl_DoxPlus_rep3

description:
Aml12_inducible_15
Inducible_counts.txt


title: Patient6, pre CART-cell Treatment, scRNAseq

description: 10x Genomics


title: Patient5, post CART-cell Treatment, scRNAseq

description: 10x Genomics


title: NZO_8_Adipose_GT19_33943


title: NZO_6_Adipose_GT19-33781


title: Aml12_shCtrl_DoxPlus_rep1

description:
Aml12_inducible_13
Inducible_counts.txt


title: Patient5, pre CART-cell Treatment, scRNAseq

description: 10x Genomics


title: Aml12_shLinc_DoxMinus_rep3

description:
Aml12_inducible_12
Inducible_counts.txt

value: Restored


title: Patient7, post CART-cell Treatment, scRNAseq

description: 10x Genomics


title: PDAC validation experiment 1, D7, row 5, hash


title: NZO_5_Adipose_GT19_33893


title: NZO_4_Adipose_GT19_33956


title: Patient3, post CART-cell Treatment, scRNAseq

description: 10x Genomics


title: Patient3, pre CART-cell Treatment, scRNAseq

description: 10x Genomics


title: Aml12_shLinc_DoxMinus_rep1

description:
Aml12_inducible_10
Inducible_counts.txt


title: Aml12_shLinc_DoxMinus_rep2

description:
Aml12_inducible_11
Inducible_counts.txt


title: Aml12_shCtrl_DoxMinus_rep3

description:
Aml12_inducible_9
Inducible_counts.txt


title: PDAC validation experiment 1, D7, row 4, hash


title: NZO_3_Adipose_GT19_34046


title: PDAC validation experiment 1, D7, row3, hash


title: PDAC validation experiment 1, D7, row 6, hash


title: NZO_2_Adipose_GT19-33772


title: Patient1, pre CART-cell Treatment, scRNAseq

description: 10x Genomics


title: PDAC validation experiment 1, D7, row 1, hash


title: Patient1, post CART-cell Treatment, scRNAseq

description: 10x Genomics


title: PDAC validation experiment 1, D7, row 2, hash


title: Aml12_shCtrl_DoxMinus_rep2

description:
Aml12_inducible_8
Inducible_counts.txt


title: PDAC compressed screen, plate 2 column 8, cDNA


title: NOD_8_Adipose_GT19_33901


title: Aml12_shCtrl_DoxMinus_rep1

description:
Aml12_inducible_7
Inducible_counts.txt


title: Bladder tumor, patient 9 CytAssist

city: Chicago

first: Thomas

last: Gajewski

state: IL

address: 929 E 57th St

institute: University of Chicago

description:
10X Visium CytAssist
TG_AZ_counts_merged.tsv.gz
code_summary.R

data_processing:
Demultiplexing, barcode processing, and raw counts were generated using Space Ranger v2.1.1 from 10X Genomics (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Downstream sample processing was carried out in R using the Seurat and Giotto packages.
Sample B13 was separated from sample B12 based on the image coordinates in the Seurat object, with column coordinates > 111 corresponding to sample B13
R code replicating analyses in the paper is also included as a supplemental file (code_summary.R).
Assembly: GRCh38 (using 10X probe set: Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv)
Supplementary files format and content: Tab-separated raw count matrix with genes in rows and barcodes in columns. Processed files also include the original images (TIF) and alignments using 10X's Loupe Browser (.json files)
Supplementary files format and content: Supplementary metadata file is a tab-delimited matrix matching samples to barcodes and tissue descriptions.
Library strategy: Visium 10X Genomics strategy

source_name: FFPE bladder tumor

extract_protocol:
Allprep DNA/RNA FFPE kit (Qiagen, Cat. # 80234), following manufacturer's protocols
Visium 10X Genomics with CytAssist, following manufacturer's protocols

value: FFPE bladder tumor

value: invasive bladder carcinoma


title: Bladder tumor, patient 10 sample 2, and patient 1 sample 2 (CytAssist)


title: NZO_1_Adipose_GT19_34210


title: PDAC compressed screen, plate 2 column 7, cDNA

value: pancreas

value: PDAC organoid


title: Aml12_shLinc_NoDox_rep3

description:
Aml12_inducible_6
Inducible_counts.txt

value: No Dox


title: NOD_6_Adipose_GT19_33934


title: PDAC compressed screen, plate 2 column 6, cDNA


title: Aml12_shLinc_NoDox_rep2

description:
Aml12_inducible_5
Inducible_counts.txt


title: Aml12_shLinc_NoDox_rep1

description:
Aml12_inducible_4
Inducible_counts.txt


title: Aml12_shCtrl_NoDox_rep3

description:
Aml12_inducible_3
Inducible_counts.txt


title: Bladder tumor, patient 7 CytAssist


title: PDAC compressed screen, plate 2 column 5, cDNA


title: PDAC compressed screen, plate 2 column 4, cDNA


title: Bladder tumor, patient 5 and patient 6 CytAssist


title: NOD_5_Adipose_GT19_34064


title: NOD_4_Adipose_GT19_34177


title: PDAC compressed screen, plate 2 column 3, cDNA


title: Bladder tumor, patient 4 CytAssist


title: Aml12_shCtrl_NoDox_rep2

description:
Aml12_inducible_2
Inducible_counts.txt


title: PDAC compressed screen, plate 2 column 2, cDNA


title: NOD_2_Adipose_GT19_34080


title: Aml12_shCtrl_NoDox_rep1

description:
Aml12_inducible_1
Inducible_counts.txt


title: Bladder tumor, patient 3 CytAssist


title: Bladder tumor, patient 2 CytAssist


title: NOD_7_Adipose_GT19_34074


title: PDAC compressed screen, plate 2 column 1, cDNA


title: NOD_1_Adipose_GT19_34230


title: PDAC compressed screen, plate 1 column 8, cDNA


title: RNA-seq of LV-SNORA28-3

first: Zhidong

last: Wang

address: Yard 27, Taiping Road, Haidian district

institute: Graduate Collaborative Training Base of Academy of Military Sciences, Hengyang Medical School, University of South China

description: The 2150bp paired-end sequencing (PE150) was performed on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.


title: Bladder tumor, patient 8 CytAssist

data_processing: Supplementary files format and content: Supplementary metadata file is a tab-delimited matrix matching samples to barcodes and tissue descriptions.


title: WBC_sAH103

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

data_processing:
The FASTQ data files were aligned to the human reference sequence (refdata-gex-GRCh38-2020-A) using 10X Genomics CellRanger on the NIH HPC Biowulf cluster. (http://hpc.nih.gov).
Seurat package (version 4.0) was used to further analyze all the single cell RNA seq data (6). Cells expressing high mitochondria genes (>10%) and cells with low quality (unique feature counts over 7,500 or less than 200) were filtered out. 51,361 features across 87,105 filtered cells were normalized and highly variable genes were identified via the FindVariableFeatures function.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: .h5

source_name: White blood cells

extract_protocol:
Venous blood was procured into EDTA-coated tubes. Within one hour of collection, red blood cells were lysed using ammonium chloride buffer (1:20, BioLegend®) for 10 minutes and the resulting WBCs were washed twice with PBS. Thin (1cm) liver sections were taken from the right lobe of explanted livers. The tissues were coarsely minced before 1 wash with PBS to remove excess red blood cells and albumin. The washed tissues were suspended in a 0.1% collagenase/0.025% hyaluronidase solution and incubated at 37ᵒC with constant agitation for 30 minutes. After incubation, tissue homogenates were centrifuged at 50g for 2 minutes to pellet debris and the resulting supernatant was collected and washed with PBS. Using OptiPrep® and DMEM, the density of the cell pellet was adjusted to ρ=1.5 and floated through discontinuous layers of ρ=1.2 and PBS. Viable liver cells were collected from the ρ=1.2/PBS interface, washed with PBS.
Liver cells (6 samples) and WBCs (7 samples) from AC and sAH patients were loaded in the lanes using 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 with a single capture lane per sample targeting recovery of 8,000 cells. All subsequent steps of library preparation and quality control were performed according to the 10X Genomics Chromium Single Cell 3' Reagent Kits User Guide. Sequencing was performed on an Illumina NovaSeq S4 at GENEWIZ (Azenta US, Inc.).

value: White blood cells


title: RNA-seq of LV-SNORA28-2


title: PDAC compressed screen, plate 1 column 7, cDNA


title: Cast_7_Adipose_GT19_33898

first: Gary

last: Churchill

address: 600 Main St

institute: The Jackson Laboratory


title: Aml12_shFalcor _rep1

description:
L30-1
sh_counts.txt


title: NOD_3_Adipose_GT19-33774


title: RNA-seq of LV-SNORA28-1


title: Cast_6_Adipose_GT19_34244


title: WBC_sAH101


title: PDAC compressed screen, plate 1 column 6, cDNA


title: WBC_sAH102


title: PDAC compressed screen, plate 1 column 5, cDNA


title: Cast_5_Adipose_GT19_34156


title: RNA-seq of LV-NC-2


title: WBC_AC29


title: WBC_AC28


title: PDAC compressed screen, plate 1 column 4, cDNA


title: PDAC compressed screen, plate 1 column 3, cDNA


title: Cast_3_Adipose_GT19_33972


title: RNA-seq of LV-NC-1


title: Cast_2_Adipose_GT19_34025


title: Cast_8_Adipose_GT19_33864


title: PDAC compressed screen, plate 1 column 2, cDNA


title: zebrafish larvae exposed to 10 uM Valbenazine

city: Wenzhou

first: Guan

last: Kaiyu

state: Zhejiang Sheng

address: 128 Xueshiqian Road, Ouhai District

institute: Wenzhou Seventh People's Hospital

data_processing:
Using the reference genome as the reference sequence
HISAT2 was used to compare the sequencing sequence after quality control with the reference genome.
The alignment results were statistically analyzed using RSeQC.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include read values for each Sample.

organism: Danio rerio

source_name: whole body

extract_protocol:
The total RNA was isolated using RNAiso Plus from control group and VBZ exposed group (10 μM), each containing 50 larval fish.
RNA was harvested using RNAiso Plus (TaKaRa). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: whole body

value: 10 uM Valbenazine


title: WBC_AC27


title: Cast_1_Adipose_GT19_34128


title: Liver_sAH104

value: Liver


title: WBC_sAH104


title: PDAC compressed screen, plate 1 column 1, cDNA


title: B6_8_Adipose_GT19_34087


title: RNA-seq of LV-NC-3


title: leaf_h2az+HsH2A.Z.1_input

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

data_processing:
Reads were trimmed of adapter content using and mapped to the Arabidopsis thaliana Col-PEK genome assembly using Bowtie2 with the following parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Aligned reads were converted to the BAM file format and quality filtered using Samtools. Duplicate reads were removed using Picard markDuplicates. For visualization, deduplicated BAM files of each genotype were converted to bedgraph files using bedtools bamtobed followed by genomecov. Samples were then normalized to the lowest read depth and converted to BigWig using bedGraphToBigWig. Finally, the signal from each sample was expressed as the log2 ratio relative to the corresponding input using bigWigCompare with –psuedocount = 1 to avoid 0/x.
Assembly: Col-PEK
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: third or fourth pair of rosette leaves

growth_protocol: Plants were grown in soil in growth chambers at +20°C under a 16 hour-light/8-hour dark cycle.

extract_protocol:
Chromatin of immunoprecipitated as described previously [ Zhao L, et al. 2020], with following modifications: 1) For each sample, 0.5 grams of leaf tissue was used, 2) ground samples were lysed in 600 μl of buffer S, 3) around 400 μl of the slurry were transferred to 0.6 ml tubes and sonicated in the Bioruptor (Diagenode) at + 4°C for 1 hour on the “high” setting with sonication intervals set to 45 seconds on/15 seconds off, 4) The sonicated lysates were centrifuged at 20,000xg for 10 min at + 4°C and 300 μl of the supernatants were transferred to a fresh 5 ml tube where 2.7 ml of buffer F was added and mixed well, 5) 50 μl of this mixture was saved as the input sample while 1.5 ml was used for immunoprecipitation with specific antibodies, 6) Arabidopsis-specific H2A.Z antibody  [Deal R, et al. 2007] and human-specific H2A.Z antibody (Abcam, ab188314) were added to the diluted lysates at a final concentration of ~2 μg/ml and incubated overnight at + 4°C with rocking, 7) 25 μl of washed Protein A dynabeads were added to each sample and incubated at + 4°C for 2 hours with rocking, 8) immunoprecipitated DNA fragments were purified using Qiagen Minelute kit and eluted in 14 μl of elution buffer. Eluted DNA samples were quantified using Picogreen reagents.
ChIP-seq libraries were prepared starting with ~1000 picograms of ChIP or input DNA samples using the ThruPlex DNA-seq kit (Takara) according to the manufacturer’s instructions. Libraries were pooled together and sequenced using paired-end 150 nt reads on an Illumina NovaSeq 6000 instrument.

value: third or fourth pair of rosette leaves

value: input


title: zebrafish larvae exposed to solvent control DMSO

value: WT

value: control DMSO


title: B6_7_Adipose_GT19_34013


title: leaf_h2az+AtHTA11_input


title: PDAC compressed screen, plate 2 column 7, hash


title: Liver_sAH103


title: B6_6_Adipose_GT19_34260


title: leaf_WT_input


title: PDAC compressed screen, plate 2 column 8, hash


title: Liver_sAH101


title: Liver_sAH102


title: PDAC compressed screen, plate 2 column 6, hash


title: B6_5_Adipose_GT19_33989


title: Liver_sAH100


title: leaf_WT_AtH2AZ_1


title: Liver_AC29


title: B6_3_Adipose_GT19_33985


title: PDAC compressed screen, plate 2 column 4, hash


title: leaf_h2az+HsH2A.Z.1_HsH2AZ_2


title: PDAC compressed screen, plate 2 column 3, hash


title: B6_2_Adipose_GT19_34158


title: human_scRNAseq_tdln2

city: Durham

first: Brent

last: Hanks

state: North Carolina

address: 308 Research Dr

institute: Duke University

description: 10x Genomics 3' Gene Expression

data_processing:
cellranger-6.0.1
Assembly: GRCh38-3.0.0
Supplementary files format and content: tab seperated values and matrix

source_name: Human Sentinel Lymph Node

extract_protocol:
Following specimen biposy, single cells were dissociated and frozen in 90% FBS 10% DMSO. Samples were then thawed at 37 degrees C and washed prior to continuing with Single Cell 3' gene expression v3
10x Genomics  Single Cell 3' v3

value: Human Sentinel Lymph Node

value: Dendritic Cells


title: leaf_h2az+HsH2A.Z.1_HsH2AZ_1


title: human_scRNAseq_tdln1

description: 10x Genomics 3' Gene Expression


title: PDAC compressed screen, plate 2 column 2, hash


title: leaf_h2az+AtHTA11_AtH2AZ_2


title: B6_1_Adipose_GT19_34264

city: Bar Harbor

value: adipose

value: 45 percent fat


title: leaf_WT_AtH2AZ_2


title: AJ_8_Adipose_GT19_33939


title: leaf_h2az+AtHTA11_AtH2AZ_1


title: LN1

description: Spatial transcriptomics processed using the 10x Genomics Visium protocol

data_processing:
Sequencing was demultiplexed, the barcodes were identified and the genes were counted using the spaceranger 2.1 pipeline (https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/inputs/fastqs-generating-fastqs)
Assembly: GRCh38-3.0.0
Supplementary files format and content: tab seperated values and matrix files
Supplementary files format and content: jpg image file of analyzed tissue
Library strategy: Spatial transcriptomics

source_name: Sentinel Lymph Node

extract_protocol:
Sentinel lymph nodes biopsies were embedded in OCT and flash frozen in liquid nitrogen prior to sectioning and mounting on 10x genomics visium slides
Libraries were constructed using the Visium Spatial 3' v1 protocol
Libraries sequenced using paired-end, dual indexed following 10x Genomics protocol

value: Sentinel Lymph Node


title: AJ_6_Adipose_GT19_34014


title: PDAC compressed screen, plate 2 column 1, hash


title: B6_4_Adipose_GT19_34083


title: leaf_WT_2 (h2a.z + HsH2A.Z control)

data_processing:
Reads were trimmed of adapter content using Trimgalore. Trimmed reads were mapped to the Arabidopsis thaliana TAIR10 genome assembly, converted to the BAM file format, and sorted by coordinate using STAR. Aligned reads were indexed and quality filtered using Samtools. Mapped fragments overlapping with exons were counted using featureCounts. Gene counts were then analyzed for differential enrichment using DESeq.
Reads were trimmed of adapter content using Trimgalore. Trimmed reads were mapped to the Arabidopsis thaliana TAIR10 genome assembly, converted to the BAM file format, and sorted by coordinate using STAR. Aligned reads were indexed and quality filtered using Samtools. Mapped fragments overlapping with exons were counted using featureCounts. Gene counts were then analyzed for differential enrichment using DESeq.
Assembly: TAIR10
Supplementary files format and content: tab delimited text file including raw read counts at each TAIR10 gene via featureCounts

extract_protocol:
Total RNA was extracted per the RNeasy Plant Mini kit (Qiagen). An RLT suspension of frozen leaf powder was split into three equal aliquots of 400 μl for 3 replicates. Total RNA was DNase-treated (Ambion) and quantified using Nanodrop One (Thermo Scientific). 100 nanograms for each of the three replicates from every sample were then used as input to generate RNA-seq libraries following the Universal RNA-seq with NuQuant protocol (Tecan).
RNA-seq libraries were constructed following the Universal RNA-seq with NuQuant protocol (Tecan).


title: LN2


title: AJ_5_Adipose_GT19_34247


title: PDAC compressed screen, plate 1 column 8, hash


title: leaf_WT_3 (h2a.z + HsH2A.Z control)


title: PDAC compressed screen, plate 2 column 5,hash


title: LN0


title: Bladder tumor, patient 1 sample 1

description:
10X Visium
TG_AZ_counts_merged.tsv.gz
code_summary.R

data_processing:
Demultiplexing, barcode processing, and raw counts were generated using Space Ranger v1.3.0 from 10X Genomics (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Downstream sample processing was carried out in R using the Seurat and Giotto packages.
R code replicating analyses in the paper is also included as a supplemental file (code_summary.R).
Assembly: GRCh38 (using 10X probe set: Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv)
Supplementary files format and content: Tab-separated raw count matrix with genes in rows and barcodes in columns. Processed files also include the original images (TIF) and alignments using 10X's Loupe Browser (.json files)
Supplementary files format and content: Supplementary metadata file is a tab-delimited matrix matching samples to barcodes and tissue descriptions.
Library strategy: Spatial transcriptomics

extract_protocol:
Allprep DNA/RNA FFPE kit (Qiagen, Cat. # 80234), following manufacturer's protocols
Visium 10X Genomics, following manufacturer's protocols

value: FFPE bladder tumor

value: invasive bladder carcinoma


title: PDAC compressed screen, plate 1 column 6, hash

value: pancreas

value: PDAC organoid


title: leaf_WT_1 (h2a.z + HsH2A.Z control)


title: PDAC compressed screen, plate 1 column 5, hash


title: PDAC compressed screen, plate 1 column 7,hash


title: Bladder tumor, patient 10 sample 1


title: AJ_3_Adipose_GT19_34213


title: leaf_h2az+HsH2A.Z.1_3


title: AJ_4_Adipose_GT19_33888


title: S18: Meningoma

city: Guangzhou

first: by

last: h

address: Guangzhou, Guangdong Province

institute: Jinan University

data_processing:
The Cell Ranger takes FASTQ files and performs alignment, filtering, barcode counting, and UMI counting
The Seurat analyses data
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Meningoma

extract_protocol:
The isolation of single cells was conducted in a sterile environment with the instruments pre-autoclaved and the solutions filtered through a 0.22μm filter. The fresh human meningioma tissues were put in cold L-isolation buffer (DPBS, 0.9mm CaCl2, 0.49mm MgCl2, 25mm D-glucose, then 1mm Sodium pyruvate), cut into small blocks of 3–5mm3 with a surgical blade, and placed after upside-down using pre-cooled PBS in a 50ml centrifuge tube. After most of the lumps sank, the supernatant containing a large number of cells related to the hematological system was discarded and repeated three to five times to obtain a relatively pure meningioma tissue mass. The tissue masses were placed in Petri dishes, minced as much as possible with a surgical blade, and transferred to a pre-cooled L-isolation buffer, where Dounce Tissue Grinder (Wheaton) was used to further mill the tissue masses into tissue suspension. The suspension was centrifuged at 2000g for 10 minutes and resuspended in a WASH buffer (L-isolation buffer containing 10% BSA). A 100μm cell screen was used for filtration to remove the uncrushed lumpy tissue and the filtrate was further filtered through a 40μm cell screen (Falcon) to obtain a crude cell suspension. After the crude suspension was washed twice with pre-cooled HBSS containing calcium and magnesium, the precipitate was resuspended in Digesting Buffer I (HBSS, 4%Dispase, 1mg/mL Collagen ASE I, 1mg/mL Collagen ASE II, 1mg/mL Collagen ASE IV, 5μg/mL DNA ASE I) and digested slowly in a rotating oven at 37°C for 1h. After digestion, the samples were centrifuged at 500g for 5 minutes at low temperature, and the cell pellets were washed twice with HBSS and re-suspended in Digest Buffer II (HBSS, Neurological Isolation Enzyme, 5μg/mL DNA ASE I) for digestion by slow rotation in an incubator at 37°C for 1h. Once the digestion was complete, the filtrate was filtered through a 15μm cell screen (Pluriselect) and the filtrate became the single-cell suspension. After low-temperature centrifugation, the single-cell suspension was re-suspended in L-isolation buffer, and then every 700g/μl of suspension was slowly added to 1.6ml of L-isolation buffer containing 20%percoll, and the suspension was centrifuged at 0, 700g for 10 min to remove tissue debris and dead cells. The cell precipitate was directly resuspended in erythrocyte lysis buffer, treated at normal temperature for 10 minutes, washed with PBS twice, and then re-suspended in pre-cooled PBS. The obtained meningioma single cells were used for single-cell sequencing. For the primary culture of meningioma cells, the tissues were directly cut into pieces, added to a DMEM medium containing 10mg/ml Collagenase I and 5%FBS, and placed in an incubator at 37°C for digestion for 1h, during which the tissues were gently blown several times every 10 minutes using a Pap pipette. The digested cells were stripped of red blood cells with red blood cell lysates, washed twice with PBS, and resuspended in DMEM/F12 (3: 1) medium containing 10%FBS(Gbico), 10% HS (Horse serum) and 1% p/s. Cells were incubated at 37°C with 5% CO2 and the medium was changed every three days.
According to the manufacturer’s instructions, single-cell libraries were generated via the Chromium Controller and the Single Cell Reagent Kit 3’ v3 (10x Genomics, Pleasanton, CA),RNA libraries were prepared for sequencing using standard Illumina protocols

value: Meningoma

value: tumor

tag: grade

value: grade III


title: AJ_2_Adipose_GT19_33852


title: PDAC compressed screen, plate 1 column 4, hash

city: Cambridge


title: S17: Meningoma


title: 129_9_Adipose_GT19_34195


title: leaf_h2az+HsH2A.Z.1_1


title: S15: Meningoma


title: PDAC compressed screen, plate 1 column 1, hash


title: leaf_h2az_3

data_processing:
Reads were trimmed of adapter content using Trimgalore. Trimmed reads were mapped to the Arabidopsis thaliana TAIR10 genome assembly, converted to the BAM file format, and sorted by coordinate using STAR. Aligned reads were indexed and quality filtered using Samtools. Mapped fragments overlapping with exons were counted using featureCounts. Gene counts were then analyzed for differential enrichment using DESeq.
Assembly: TAIR10
Supplementary files format and content: tab delimited text file including raw read counts at each TAIR10 gene via featureCounts

extract_protocol:
Total RNA was extracted per the RNeasy Plant Mini kit (Qiagen). For h2a.z plants, above ground tissue from three different plants was harvested and individually processed to extract total RNA following the manufacturer’s recommendations. For all others, an RLT suspension of frozen leaf powder was split into three equal aliquots of 400 μl for 3 replicates. Total RNA was DNase-treated (Ambion) and quantified using Nanodrop One (Thermo Scientific). 100 nanograms for each of the three replicates from every sample were then used as input to generate RNA-seq libraries following the Universal RNA-seq with NuQuant protocol (Tecan).
RNA-seq libraries were constructed following the Universal RNA-seq with NuQuant protocol (Tecan).


title: PDAC compressed screen, plate 1 column 3, hash


title: leaf_h2az_2


title: S16: Meningoma


title: 129_6_Adipose_GT19_33895


title: S14: Meningoma

value: grade II


title: leaf_h2az+HsH2A.Z.1_2

value: third or fourth pair of rosette leaves


title: S13: Meningoma


title: Control_DMSO2_D2

description:
Control_DMSO.bw
Control_DMSO_N_peaks.narrowPeak

data_processing:
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
Bowtie2 (Langmead et al. 2012) was applied on trimmed read pairs to map reference genome (hg38) with the following setup: --dovetail –no-unal –no-mixed –no-discordant –very-sensitive -I 0 -X 1000.
After getting sam alignment files from Bowtie2, the files were converted to bam files using “samtools view -S -b” (Li et al. 2015). Bamfiles  were further purified by removing PCR duplicates using following settings: “picard MarkDuplicates REMOVE_DUPLICATES=true” and mitochondrial reads (http://broadinstitute.github.io/picard/).
Peak calling was used applying MACS2 (Zhang et al. 2008) using following setting: Macs2 call peak -f BAMPE -m 4 100 –bdg –SPMR (for narrow peak).
Bigwigs were generated using bins using deeptools bamCoverage with the following parameters: --normalizeUsing RPKM
Assembly: Hg38
Supplementary files format and content: Coverage in bigWig format
Supplementary files format and content: peak calls in narrowPeak
Library strategy: NicE-seq

extract_protocol:
Cells were fixed with 1% Formaldehyde
For library construction, MTU87 or LTAU87 cells with or without belinostat treatment were cross-linked using 1% formaldehyde for 10 min at room temperature and quenched by using 125 mM glycine. Nuclei were isolated by incubating the cross-linked cells in cytosolic buffer (15 mM Tris-HCl pH 7.5, 5 mM MgCl2, 60 mM KCl, 0.5 mM DTT, 15 mM NaCl, 300 mM sucrose, and 1% NP40) for 10 min on ice with occasional agitation. Nuclei were precipitated by spinning at 1000 × g, 4 °C for 5 min and the supernatant was discarded. Open chromatin DNA was labeled with biotin by incubating the nuclei in the presence of 2.5 U of Nt.CviPII (NEB R0626S), 10 U of DNA polymerase I (M0209S) and 30 μM of each dNTP including 6 μM of biotin-14-dATP (Invitrogen, 19524-016) and 6 μM of biotin-16-dCTP (ChemCyte, CC-6003-1) in 200 μL of 1× NEB buffer 2. The labeling reaction was carried out at 37 °C in a thermo-mixer at 800 RPM for 2 h. We added 20 μL of 0.5 M EDTA and 2 μg of RNase A to the labeling reaction and incubated it at 37 °C for 0.5 h to stop the reaction and digest RNA. Finally DNA–protein cross-linking was reversed by adding 20 μL of proteinase K (NEB, P8107S) and 20 μL of 20% SDS to the reaction and incubating at 65 °C for overnight. Biotin-labeled genomic DNA was extracted using phenol chloroform.                Biotin-labeled genomic DNA were sonicated into 150-bp fragments (Covaris) and 1 μg of DNA was end-repaired, dA-tailed, and ligated with NEB Illumina adaptor (E7370S). Without further purification, the ligation product was mixed with 50 μL of Streptavidin magnetic beads (Invitrogen 65001, blocked using 0.1% cold fish gelatin in 1× PBS overnight at 4 °C) in 1 mL of B&W buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl). Biotin-labeled open chromatin DNA was captured by streptavidin magnetic beads at 4 °C for 2 h with end-over-end rotation. The beads were washed four times with B&W buffer plus 0.05% of Triton X-100 followed by one wash with TE plus Triton X-100. The beads were resuspended in 40 μL of nuclease-free water and 4 μL was used for library amplification using PCR (NEB, E7370S). Ten PCR cycles were usually sufficient to generate the amount of library DNA needed for sequencing.

value: Brain

value: Glioblastoma


title: leaf_h2az_1


title: Control_DMSO1_D2


title: leaf_h2az+AtHTA11_2


title: 129_7_Adipose_GT19_34030


title: 129_4_Adipose_GT19_33945


title: S11: Meningoma


title: 129_3_Adipose_GT19_33851


title: S12: Meningoma


title: 129_2_Adipose_GT19_33811


title: AJ_1_Adipose_GT19_34017


title: leaf_h2az+AtHTA11_1


title: S10: Meningoma

value: grade I


title: PDAC compressed screen, plate 1 column 2, hash

data_processing:
The demultiplexing, barcoded, processing, gene counting and aggregation were made using the STARsolo workflow (https://dockstore.org/workflows/github.com/lilab-bcb/cumulus/STARsolo:2.0.0?tab=info) and CITEseq-count (https://portal.firecloud.org/?return=terra#methods/bemead/CITEseq-count/7) on Terra
Assembly: hg38
Supplementary files format and content: tab separated value files and matrix files


title: Control_Bel2_D2

description:
Control_Bel.bw
Control_Bel_N_peaks.narrowPeak


title: Control_DMSO1_D1


title: leaf_WT_3

value: WT


title: S9: Meningoma


title: Control_Bel2_D1


title: 129_1_Adipose_GT19_34179


title: AJ_7_ORSAM11446_GT20-13783_heart

source_name: heart

value: heart

value: 45percent fat


title: leaf_WT_2


title: Control_Bel1_D2

source_name: Brain


title: S8: Meningoma


title: Control_Bel1_D1


title: leaf_WT_1


title: WSB_8_ORSAM11444_GT20-13797_heart


title: WSB_9_ORSAM11445_GT20-13825_heart